My mother hired a licensed, bonded, and insured roofing contractor to clean the gutters on her flat roof in NY. She was told that she needed a new roof, so the company removed the old roof and installed a new one with SBS black modified bitumen membrane in February 2009. My mom never had any problems with this roof until this roofing company (who has been around since 1921) worked on her roof. Ponded water remains on her roof for more than 48 hours, and this has resulted in paint peeling, cracking, & chipping on the walls, ceilings, and beams to the second floor.
There is no attic on this house, and it is approximately 100 years old. My mother still has 7 years left on her warranty, but the roofing company is saying that this damage occurred before they fixed her roof. They insist that the house is very old and out of level, and that they have provided my mother with a water tight roofing system that does not leak, and ponded water is nothing to be concerned about. If the house isn't leaking why would there be dark stains which look like mold/mildew and why would there be damages present now that didn't exist prior to 2009. I am being told by another roofing company that 2 beams on the roof have collapsed.
Would a roofing contractor rip off an old roof down to the plywood and install a new roof over it if? I live in Florida, and am trying my best to help my mom with this problem. The BBB has not been of much help. My mom is 84 yrs old, disabled, and lives alone and I feel that she has been taken advantage of not to mention is this house safe for her to live in? Any help will be greatly appreciated. Have loads more photos if needed.

First thing that needs to be done is to verify that it is an active leak. The area should be probed with a moisture meter to see if it is indeed wet. Then you have a position you can negotiate from with the roofing company that installed the roof. Try calling a structural engineer or another roofing company, it may cost a few dollars for a inspection, but at this point it may be money well spent.

While a Flir (thermal image) camera is a good tool, almost as important is a moisture meter. Flir does not identify moisture, it sees temperature differences. Moist and cold will usually show up close to the same, thats why it's important to use a meter to determine if it is in fact wet. As InspectorD said, try calling a home inspector in her area with all the toys to identify moisture problems.

This drywall has to be removed either way. Take some more pictures so you can show landmarks in the house so you can prove that these pictures are from this house. If this damage was done with water leaking before the new roof an insurance claim should have been made. As no one was aware of it, it may not be to late. If you remove the damaged drywall and you find water leaking when it rains it will be hard for the roofing company to argue. If you beleive this is new, you could call the insurance company, they send in people to repair the dammage inside.

That's definitely a great idea; however my mom already called the insurance company and they told her that her policy does not cover first party (property) damages. If I am understanding all of this correctly, a building inspector should use a moisture meter to see if there is an active leak and he would also inspect the roof. Then, I would have to call someone in to remove the drywall but not replace it until we can see if there is water leaking. What is the probability of not seeing water leaking; since there are water leaks that are invisible to the human eye? Also would I be able to remove the drywall by using a hammer to rip open the ceilings or walls or is that not a good idea because of wiring,plumbing, and other various concerns? Would you also suggest doing the same thing re: the beams or is that not recommended since it is part of the roof structure and I don't have any idea how to treat the mold/mildrew growth.